High-definition spatial transcriptomics for in situ tissue profiling
chevron_leftchevron_right
Catalog
Dataset information
Contributors
Accessions
Dataset information
Summary:
Tissue function relies on the precise spatial organization of cells characterized by distinct molecular profiles. Single-cell RNA-Seq captures molecular profiles but not spatial organization. Conversely, spatial profiling assays to date have lacked global transcriptome information, throughput or single-cell resolution. Here, we develop High-Density Spatial Transcriptomics (HDST), a method for RNA-Seq at high spatial resolution. Spatially barcoded reverse transcription oligonucleotides are coupled to beads that are randomly deposited into tightly packed individual microsized wells on a slide. The position of each bead is decoded with sequential hybridization using complementary oligonucleotides providing a unique bead-specific spatial address. We then capture, and spatially in situ barcode, RNA from the histological tissue sections placed on the HDST array. HDST recovers hundreds of thousands of transcript-coupled spatial barcodes per experiment at 2 μm resolution. We demonstrate HDST in the mouse brain, use it to resolve spatial expression patterns and cell types, and show how to combine it with histological stains to relate expression patterns to tissue architecture and anatomy. HDST opens the way to spatial analysis of tissues at high resolution.Overall design:
Three sections of the main olfactory bulb from adult C57BL/6J miceTechnology:
HDST
Platform:
Illumina NextSeq 500
Species:
Mus musculus
Tissues:
Brain
Development stage:
12 weeks
Citation:
Vickovic, Sanja et al. “High-definition spatial transcriptomics for in situ tissue profiling.” Nature methods vol. 16,10 (2019): 987-990. doi:10.1038/s41592-019-0548-ySubmission date: 2019-05-03Update date: 2019-09-20
Sample number: 3
Contributors
Sanja Vickovic; Ludvig Bergenstråhle
Contact: vickovic@broadinstitute.org
Accessions
GEO Series Accessions:
GSE130682